PROJECT SUMMARY/ABSTRACT: Alzheimer's disease (AD) is the leading cause of age-related neurodegeneration. Its prevalence is predicted to greatly increase with the increasing numbers of elderly in the United States. While histological hallmarks of AD are well characterized, the mechanisms of AD are still unclear. Recent studies have characterized the transcriptional and epigenetic alterations in post-mortem brains of AD patients. This work suggests that epigenetics changes, induced by a combination of external stressors and aging, contribute to AD progression. DNA methylation is a covalent modification to DNA and an epigenetic mark with the capacity to induce long- lasting changes to gene expression. Reproducible alterations to DNA methylation at specific genomic regions have been associated with AD in large patient cohorts, including at genomic segments adjacent to genes with AD susceptibility variants. The functional importance of these changes, however, has been difficult to assess. Heterogeneity in sample composition, disease course, and genetic background are confounding factors, as is the stochastic nature of epigenetic lesions at the level of the individual cell. These limitations have prevented meaningful correlations of epigenotype and phenotype and thwart identification of epimutations that functionally contribute to the Alzheimer's disease state. There is need for a tractable, genetically controlled AD model system in disease-relevant human cell types that allows for assessment of DNA methylation status at single cell resolution. To this end, this proposal aims to develop and characterize an in vitro model of AD neurons derived from human induced pluripotent stem cells (hiPSCs). Ongoing work is being completed to define in vitro culture conditions that induce methylation changes at AD-associated differentially methylated regions (DMRs). This will allow for the assessment of the role of AD-DMRs in regulating gene expression with potential to alter AD phenotypes. A combination of genetic and culture condition based stressors that mimic AD are being used in conjunction with the Reporter of Genomic Methylation (RGM), our recently developed genetic tool for assessing DNA methylation at single-cell resolution. By inserting the RGM adjacent to an AD-DMR, it is possible to isolate cells with a specific DNA methylation perturbation and correlate transcriptional and molecular phenotypes. The proposed experiments will be the first to systematically characterize factors that contribute to the epigenetic alterations in AD. This work will also provide previously unobtainable resolution to the correlation of DNA methylation and transcriptional changes associated with disease. Finally, a model of the induction of AD- associated epigenetic errors will enable further basic mechanistic studies. This work will act as a stepping- stone for understanding why and how DNA methylation changes occur in neurodegenerative disorders.